Dietary eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were compared for their effects on arterial thrombus formation in vivo using a well validated rat model. Platelet aggregation (triggered by collagen or adenosine diphosphate in whole hirudinized blood), thromboxane formation (TxB 2) and platelet phospholipid fatty acid composition were measured also. Animals fed diets containing hydrogenated coconut oil or sunflower seed oil served as prothrombotic and antithrombotic controls, respectively. In a first study, rats were fed a mixture of EPA and DHA ethyl esters (MIX) in increasing amounts and results indicated that 4% of n−3 fatty acids had an optimum reducing effect on thrombosis tendency. Dietary administration of MIX further resulted in a dose-dependent promotion of disaggregation after collagen-induced aggregation, which significantly correlated with the reduction in platelet TxB 2 formation. In a subsequent comparative study, both EPA and DHA ethyl esters affected thrombosis tendency, platelet aggregation and TxB 2 formation to a similar extent. In addition, both polyenes increased the apparent thromboxane A 2-sensitivity of platelets, which appeared negatively related to arterial thrombosis tendency. We conclude that EPA and DHA have similar reducing effects on arterial thrombogenesis in vivo in rats and have comparable effects on the selected platelet functions in vitro.